Sodium in PDB 5a3w: Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca)

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca), PDB code: 5a3w was solved by V.Srikannathasan, C.Johansson, C.Gileadi, J.Kopec, C.Strain-Damerell, K.Kupinska, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.102, 142.102, 152.256, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.6

The structure of Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) (pdb code 5a3w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca), PDB code: 5a3w:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Plu-1 (JARID1B) in Complex with Pyridine-2, 6-Dicarboxylic Acid (Pdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1756 b:47.9 occ:1.00 O A:HOH2049 2.2 53.8 1.0 O A:THR416 2.5 47.1 1.0 O A:LEU413 2.7 36.6 1.0 OD1 A:ASN91 2.8 40.8 1.0 O A:GLU419 2.9 60.9 1.0 O A:HOH2051 3.2 47.6 1.0 O A:LEU90 3.3 38.7 1.0 C A:THR416 3.5 55.7 1.0 O A:VAL414 3.9 33.2 1.0 C A:LEU413 3.9 34.3 1.0 C A:GLU419 3.9 51.7 1.0 C A:VAL414 4.0 32.2 1.0 CG A:ASN91 4.0 40.7 1.0 N A:THR416 4.0 41.4 1.0 CA A:VAL414 4.1 29.7 1.0 CB A:GLU419 4.2 53.9 1.0 CA A:THR416 4.3 51.0 1.0 C A:LEU90 4.4 30.8 1.0 CA A:ASN91 4.4 36.7 1.0 N A:ILE417 4.4 68.7 1.0 N A:VAL414 4.5 27.9 1.0 CA A:GLU419 4.5 51.3 1.0 CA A:ILE417 4.6 69.2 1.0 N A:SER415 4.6 36.5 1.0 CB A:ASN91 4.7 40.2 1.0 O A:ILE417 4.7 58.9 1.0 N A:GLU419 4.7 54.5 1.0 C A:SER415 4.8 48.4 1.0 C A:ILE417 4.8 55.2 1.0 N A:ASN91 4.8 37.2 1.0 CB A:THR416 4.9 47.8 1.0 N A:ASP420 4.9 44.2 1.0 CD1 A:LEU413 4.9 67.0 1.0

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087